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Messed with the raw file and the jpeg file to get this. At least three different layer masks along the way. Here's something to try, it's not good for every cloud shot but it might give you an idea. Copy your image, de saturate the copy and then invert it. If this inverted layer is on top, try a few different layer modes on it, see what it does to the clouds. Just a hint.
Enjoy.
Mikel.